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Sample GSM2152445 Query DataSets for GSM2152445
Status Public on Jun 30, 2016
Title ATAC-seq from Mael-KD rep1
Sample type SRA
Source name Mael-KD OSC
Organism Drosophila melanogaster
Characteristics cell type: Ovarian Somatic Cells (OSC)
variation: RNAi Mael
Treatment protocol Transfection of siRNAs was performed using Cell Line 96-well Nucleofector Kit SF and 96-well Shuttle Device (Lonza).
Growth protocol Cells were grown at 26 degrees on OSC medium (Fly Extract added M3 medium).
Extracted molecule genomic DNA
Extraction protocol ATAC-seq samples were extracted as described (Buenrostro et al., 2013; Buenrostro et al., 2015).
ATAC-seq libraries were constructed as described (Buenrostro et al., 2013; Buenrostro et al., 2015).
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina MiSeq
Description processed_ATACseq.txt
Data processing Library strategy: ATAC-Seq
ATAC-seq analysis was performed as previously described (Buenrostro et al., 2013) with some modifications. Adaptors were removed using Cutadapt software, and reads with lengths shorter than 50 bp were removed. Reads were first aligned to dm3 genome using Bowtie2.0.6 (Langmead and Salzberg, 2012) with the parameter –X 4000, to allow fragments up to 4 kbp long. MACS2 (Zhang et al., 2008) was used for peak calling with the parameters –g dm –nomodel –nolambda –extsize 239 –keep-dup all. MACS2 bdgdiff was used to compare samples, and CEAS (Shin et al., 2009) was used to annotate the peaks. To analyze the ATAC-seq reads mapped to transposons, reads mapped to the genome concordantly were extracted and mapped to Repbase transposon consensus sequences (Jurka, 1998) using the same parameters as for genome mapping.
Genome_build: dm3
Supplementary_files_format_and_content: Normalized read counts mapped to each transposon consensus sequence (Tab delimited format, txt).
Submission date May 13, 2016
Last update date Jul 03, 2021
Contact name Yuka W. Iwasaki
Organization name Keio University School of Medicine
Department Department of Molecular Biology
Lab Siomi Lab
Street address 35 Shinanomachi, Shinjuku-ku,
City Tokyo
ZIP/Postal code 160-8582
Country Japan
Platform ID GPL16479
Series (1)
GSE81434 Piwi modulates chromatin accessibility by regulating multiple factors including histone H1 to repress transposons
BioSample SAMN04999511
SRA SRX1760717

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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